How did you fix it? Game restart like in a "new game" or just quit and restart? Because I tried the later and it doesn't work for me.

Can't say. Just a game restart did the trick. Also, I went and changed the value myself - a just a 4-byte value and is easy to find. BEWARE! I ran into a problem - the max stack size, for parts at least, is decimal 999. So once the game recalculates the amount you have you end up with an inventory full of parts items.

Now, the NRG problem is easy to tackle - either craft n amount if cells to refill or use the Inf. Items option (slot the cell) and just remember to use it every now and then.

So far Energy does not work, I have downloaded the HF1 version and can find NO information on what if any is the difference, purchase the Digital Deluxe version. I have yet to find any real information about this HF1 build. Going to try the plain 524.7 and see if the same problem occurs. The patch notes state that if you are having issues with the 524.7 patch, you can revert to the previous version of the game

Just on the topic of the hacking mini-game. Perhaps the best approach would be to copy what the "Stop! Worm" software does and somehow make that permanently hold. Basically stops the countermeasure in it's tracks and lets the player hack whatever they want while it's frozen.